Merge pull request #109 from KrisThielemans/remove_ids

remove unique identifiers

Author: KrisThielemans

cpp/petsird_generator.cpp

@@ -65,7 +65,6 @@ get_detector_module()
     constexpr auto N0 = NUM_CRYSTALS_PER_MODULE[0];
     constexpr auto N1 = NUM_CRYSTALS_PER_MODULE[1];
     constexpr auto N2 = NUM_CRYSTALS_PER_MODULE[2];
-    unsigned id = 0;
     for (int rep0 = 0; rep0 < N0; ++rep0)
       for (int rep1 = 0; rep1 < N1; ++rep1)
         for (int rep2 = 0; rep2 < N2; ++rep2)
@@ -74,13 +73,11 @@ get_detector_module()
                                                       { 0.0, 1.0, 0.0, (rep1 - N1 / 2) * CRYSTAL_LENGTH[1] },
                                                       { 0.0, 0.0, 1.0, (rep2 - N2 / 2) * CRYSTAL_LENGTH[2] } } };
             rep_volume.transforms.push_back(transform);
-            rep_volume.ids.push_back(id++);
           }
   }
 
   petsird::DetectorModule detector_module;
   detector_module.detecting_elements.push_back(rep_volume);
-  detector_module.detecting_element_ids.push_back(0);
 
   return detector_module;
 }
@@ -92,7 +89,6 @@ get_scanner_geometry()
   petsird::ReplicatedDetectorModule rep_module;
   {
     rep_module.object = get_detector_module();
-    uint32_t module_id = 0;
     std::vector<float> angles;
     for (unsigned int i = 0; i < NUM_MODULES_ALONG_RING; ++i)
       {
@@ -104,13 +100,11 @@ get_scanner_geometry()
           petsird::RigidTransformation transform{ { { std::cos(angle), std::sin(angle), 0.F, 0.F },
                                                     { -std::sin(angle), std::cos(angle), 0.F, 0.F },
                                                     { 0.F, 0.F, 1.F, MODULE_AXIS_SPACING * ax_mod } } };
-          rep_module.ids.push_back(module_id++);
           rep_module.transforms.push_back(transform);
         }
   }
   petsird::ScannerGeometry scanner_geometry;
   scanner_geometry.replicated_modules.push_back(rep_module);
-  scanner_geometry.ids.push_back(0);
   return scanner_geometry;
 }
 

cpp/petsird_helpers.h

@@ -41,8 +41,8 @@ expand_detection_bins(const ScannerGeometry& scanner_geometry, const T& list_of_
   const auto& rep_module = scanner_geometry.replicated_modules[0];
   assert(rep_module.object.detecting_elements.size() == 1);
 
-  // TODO currently ids are uint32_t, so use this type to avoid compiler warnings
-  const uint32_t num_el_per_module = rep_module.object.detecting_elements[0].ids.size();
+  // TODO currently det_el_idx are uint32_t, so use this type to avoid compiler warnings
+  const uint32_t num_el_per_module = rep_module.object.detecting_elements[0].transforms.size();
 
   std::vector<ExpandedDetectionBin> result;
   for (auto bin : list_of_detection_bins)

matlab/toolbox/+petsird/+helpers/expand_detection_bins.m

@@ -9,7 +9,7 @@
 assert(length(scanner_geometry.replicated_modules) == 1);
 rep_module = scanner_geometry.replicated_modules(1);
 assert(length(rep_module.object.detecting_elements) == 1);
-num_el_per_module = length(rep_module.object.detecting_elements(1).ids);
+num_el_per_module = length(rep_module.object.detecting_elements(1).transforms);
 
 expanded_det_bins = arrayfun(@(id) struct('module', idivide(id.det_el_idx, num_el_per_module), 'el', mod(id.det_el_idx, num_el_per_module)), detection_bins);
 

matlab/toolbox/+petsird/+helpers/generator.m

@@ -82,7 +82,6 @@
     detector_module = get_detector_module(cfg);
 
     rep_module = petsird.ReplicatedDetectorModule(object=detector_module);
-    module_id = 0;
     for i = 0:cfg.NUM_MODULES_ALONG_RING-1
         angle = 2 * pi * i / cfg.NUM_MODULES_ALONG_RING;
         for ax_mod = 0:cfg.NUM_MODULES_ALONG_AXIS-1
@@ -94,12 +93,10 @@
                 ]) ...
             );
             rep_module.transforms = [rep_module.transforms transform];
-            rep_module.ids = [rep_module.ids module_id];
-            module_id = module_id + 1;
         end
     end
 
-    geometry = petsird.ScannerGeometry(replicated_modules=[rep_module], ids=[0]);
+    geometry = petsird.ScannerGeometry(replicated_modules=[rep_module]);
 end
 
 function detector = get_detector_module(cfg)
@@ -109,7 +106,6 @@
     N0 = cfg.NUM_CRYSTALS_PER_MODULE(1);
     N1 = cfg.NUM_CRYSTALS_PER_MODULE(2);
     N2 = cfg.NUM_CRYSTALS_PER_MODULE(3);
-    id = 0;
     for rep0 = 0:N0-1
         for rep1 = 0:N1-1
             for rep2 = 0:N2-1
@@ -120,12 +116,10 @@
                         0, 0, 1, (rep2 - N2 / 2) * cfg.CRYSTAL_LENGTH(3); ...
                     ]));
                 rep_volume.transforms = [rep_volume.transforms transform];
-                rep_volume.ids = [rep_volume.ids id];
-                id = id + 1;
             end
         end
     end
-    detector = petsird.DetectorModule(detecting_elements=[rep_volume], detecting_element_ids=[0]);
+    detector = petsird.DetectorModule(detecting_elements=[rep_volume]);
 end
 
 function crystal = get_crystal(cfg)

model/DetectorInformation.yml

@@ -19,9 +19,6 @@ ReplicatedGenericSolidVolume: ReplicatedObject< GenericSolidVolume >
 DetectorModule: !record
   fields:
     detectingElements: ReplicatedBoxSolidVolume*
-    # list of unique ids for every replicated solid volume
-    # constraint: size(detectingElements) == size(detectingElementsIds)
-    detectingElementIds: uint*
     # optional list describing shielding/optical reflectors etc
     nonDetectingElements: ReplicatedGenericSolidVolume*
 
@@ -34,9 +31,6 @@ ScannerGeometry: !record
   fields:
     # list of different types of replicated modules
     replicatedModules: ReplicatedDetectorModule*
-    # list of unique ids for every replicated module
-    # constraint: size(replicated_modules) == size(ids)
-    ids: uint*
     # shielding etc
     nonDetectingVolumes: GenericSolidVolume*?
 

model/GeometryInformation.yml

@@ -30,9 +30,6 @@ ReplicatedObject<T>: !record
     # list of transforms
     # constraint: length >= 1
     transforms: RigidTransformation*
-    # list of unique ids for every replicated solid volume
-    # constraint: size(transforms) == size(ids)
-    ids: uint*
   computedFields:
     numberOfObjects: size(transforms)
 

python/petsird/helpers/__init__.py

@@ -43,7 +43,7 @@ def expand_detection_bins(
     assert len(scanner_geometry.replicated_modules) == 1
     rep_module = scanner_geometry.replicated_modules[0]
     assert len(rep_module.object.detecting_elements) == 1
-    num_el_per_module = len(rep_module.object.detecting_elements[0].ids)
+    num_el_per_module = len(rep_module.object.detecting_elements[0].transforms)
 
     return [
         ExpandedDetectionBin(module=bin.det_el_idx // num_el_per_module,

python/petsird/helpers/generator.py

@@ -54,7 +54,6 @@ def get_detector_module() -> petsird.DetectorModule:
     N0 = NUM_CRYSTALS_PER_MODULE[0]
     N1 = NUM_CRYSTALS_PER_MODULE[1]
     N2 = NUM_CRYSTALS_PER_MODULE[2]
-    id = 0
     for rep0 in range(N0):
         for rep1 in range(N1):
             for rep2 in range(N2):
@@ -67,11 +66,8 @@ def get_detector_module() -> petsird.DetectorModule:
                     dtype="float32",
                 ))
                 rep_volume.transforms.append(transform)
-                rep_volume.ids.append(id)
-                id += 1
 
-    return petsird.DetectorModule(detecting_elements=[rep_volume],
-                                  detecting_element_ids=[0])
+    return petsird.DetectorModule(detecting_elements=[rep_volume])
 
 
 def get_scanner_geometry() -> petsird.ScannerGeometry:
@@ -83,7 +79,6 @@ def get_scanner_geometry() -> petsird.ScannerGeometry:
     ]
 
     rep_module = petsird.ReplicatedDetectorModule(object=detector_module)
-    module_id = 0
     for angle in angles:
         for ax_mod in range(NUM_MODULES_ALONG_AXIS):
             transform = petsird.RigidTransformation(matrix=numpy.array(
@@ -94,11 +89,9 @@ def get_scanner_geometry() -> petsird.ScannerGeometry:
                 ),
                 dtype="float32",
             ))
-            rep_module.ids.append(module_id)
-            module_id += 1
             rep_module.transforms.append(transform)
 
-    return petsird.ScannerGeometry(replicated_modules=[rep_module], ids=[0])
+    return petsird.ScannerGeometry(replicated_modules=[rep_module])
 
 
 def get_detection_efficiencies(